Dark Pirate Commandos are the result of a Pirate Commando being possessed by Ing. They are an invaluable addition to the Ing Horde and only Hunter Ing are allowed to possess them (even then, they hold fierce competition for the tremendously strong bodies). Extremely powerful, they also share the Hunter Ing ability to phase out of the local time-space, "teleporting" from one location to next, leaving after images to confound their opponent; while teleporting, they are only visible through the Dark Visor. This system is similar to the one used by the Chozo Ghosts in Metroid Prime.

Dark Commandos are extremely dangerous in large groups, and often lock rooms in order to prevent escape. They should not be considered easy to defeat; they often strike ambushes in pairs later on in the game. They attack not only with their phasing skills, but also with improved versions of the standard form of the Pirate Commando weapon, a deadlier energy dagger sprouting from the tips of their weapons, and a grenade launcher on their shoulder, which fires experimental EMP grenades stolen from the slain pirates. The rooms where they attack also tend to have irregular terrains, hindering those with poor aim.

It should be noted, however, that an Entangler shot followed by a Missile will destroy them instantly.

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The Dark Pirate Commando acts in a similar manner to the Chozo Ghosts. They both phase in and out of the local timespace and they both have the ability to fire projectiles that can send static through Samus's visor. However, the Pirates can be immobilized with the Dark Beam while the Ice Beam cannot immobilize the Chozo Ghosts.

In certain areas (particularly in the light version of Torvus Bog), if the player fails to defeat all the Dark Pirate Commandos fast enough, they will give up and warp out of the room (releasing the door locks if they were active).

"The Ing prize the few Pirate Commandos they manage to take alive. Only Hunter Ing are allowed to possess the Commandos, and the competition for that right is fierce among them. The Hunter Ing ability to phase out of local timespace carries over to the Dark Pirate Commando. They will fire bursts of dark matter at enemies, along with experimental EMP grenades stolen from the Space Pirates."